[Biopython] problem parsing embl file

[Sameet Mehta]

Hi Peter,

I think i figured out a way around this.  I will of course try with
biopython 1.54 but in the line that begins with SQ (identifier for the
region where the sequence starts, the length of the true sequence is
given.  Getting that information and replacing the one on the ID line
was trivial.  I have done it.

Thanks for the help.

Sameet

On Mon, Jun 28, 2010 at 6:06 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Jun 28, 2010 at 9:58 PM, Sameet Mehta <msameet at gmail.com> wrote:
>> Yes I am indeed running v 1.53
>
> That isn't our latest release (although it may be the latest
> release available as a package from your Linux distribution).
>
>> I will change that line and see if it works, probably will.  But I
>> have multiple such files to deal with and i dont knwo the lengths of
>> each of those.
>
> Please try that and let us know if that works.
>
>> Is there any other simpler way around.
>
> Yes, upgrade to Biopython 1.54 and this length check will
> just issue a warning and carry on (unlike Biopython 1.53
> which issues an exception and stops).
>
> Regards,
>
> Peter
>



-- 
Sameet Mehta, Ph.D.,
Phone:  (301) 842-4791